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The analytic derivative of the electrostatic interaction between far separated fragments is developed and a number of restricted Hartree-Fock (RHF) geometry optimizations are performed by using the fragment molecular orbital method (FMO) and ab initio methods. The [alpha]-helix, [beta]-turn and extended conformers of a 10-residue polyanaline are analyzed and the good FMO accuracy is established.

Theoretical studies using ab initio calculations and kinetic experiments demonstrate the ability of magnesium ion to cleave a phosphorus-oxygen bond by directly coordinating with the translating oxygen. This direct coordination favors the second step of the hammerhead ribozyme reactions. A comparative study of the stabilities of oxyphosphoranes with different ionic valences reveals that stability is increased by the protonation of a dianionic species.

An analysis of a cyclic system where rotation of the equatorial bond is prohibited by cyclic ring formation during hydrolysis is presented. The complete reaction energy surface for an RNA fragment attack is discussed. Results showed a difference from acrylic systems in that the stereoelectronically unfavorable transition state TS2 did not exist because of the unique cyclic nature of the intermediate. Overall results reflected evidence of the non-existence of a oxyphosphorane intermediate in the base-catalyzed RNA hydrolysis.

Molecular dynamics simulations were performed to simulate Ca2+-dependent conformational change of calmodulin (CaM). Simulations of the fully Ca2+-bound form of CaM (Holo-CaM) and the Ca2+-free form (Apo-CaM) were performed in solution for 4 ns starting from the X-ray crystal structure of Holo-CaM. A striking difference was observed between the trajectories of Holo-CaM and Apo-CaM: the central helix remained straight in the former but became largely bent in the latter. Also, the flexibility of Apo-CaM was higher than that of Holo-CaM. The results indicated that the bound Ca2+ ions harden the structure of CaM. [Copyright &y& Elsevier]

The article presents information about a study conducted on enantiotopic differentiation in horse-liver. Some of the chemicals used in the study are, crystalline HLADH, NAD, NADH and beef liver glutamate dehydrogenase, N,N-dimethylaminomethylferrocene and silica gel for column chromatography. Each compound showed the M peak for the expected molecular formula in the MS spectrum. Active MnO2 as the oxidant was prepared according to the literature and stored as a powder after lyophilization. Melting points were measured on a hot stage and are uncorrected. Optical rotations were measured with a Jasco DIP-360 digital polarimeter.

4-Hydroxycyclohexanecarboxylate dehydrogenase, which requires NAD as a cofactor, was detected in crude soluble extracts of Corynebacterium cyclohexanicum grown on cyclohexanecarboxylic acid as the sole carbon source. The dehydrogenase was purified from extracts to an electrophoretically homogenous state by ammonium sulfate precipitation and chromatography on DEAE-650s, agarose-NAD and hydroxyapatite. The enzyme consisted of two identical subunits and had a native relative molecular mass of 53600. There were two residues each of cysteine and tryptophan in the enzyme molecule. Oxo acid rather than hydroxy acid was routinely used as substrate for assay of the enzyme. The enzyme is highly specific for 4-oxocyclohexanecarboxylic acid: the carboxyl group is essential and the position of carbonyl group is important; neither the 2-oxo nor the 3-oxo homologue was used as substrate. A methyl substitution on the ring of 4-oxocyclohexanecarboxylate resulted in an almost complete loss of its activity. The reduction product was identified as trans-4-hydroxycyclohexanecarboxylic acid by gasliquid chromatography and mass spectrometry. It was used as a substrate for the reverse reaction in the presence of NAD but not its cis-isomer. The enzyme was specific for the B-side (pro-S) hydrogen of NADH in the hydrogen transfer from NADH to 4-oxocyclohexanecarboxylate. The Km values for 4-oxocyclohexanecarboxylate and NADH in the reduction reaction at pH 6.8 were 0.50 mM and 0.28 mM, respectively, whereas those for trans-4hydroxycyclohexanecarboxylate and NAD in the oxidation reaction at pH 8.8 were 0.51 mM and 0.23 mM, respectively. The equilibrium constant of the reaction was 1.79 × 10-10 M. The enzyme was strongly inhibited by N-bromosuccinimide. [ABSTRACT FROM AUTHOR]

Presents the results of a study which examine the roles of metal ions in the enzymatic cleavage of RNA. Results of study.

Abstract: Full quantum computation of the electronic state of proteins has recently become possible by the advent of the ab initio fragment molecular orbital (FMO) method. We applied this method to the analysis of the interaction between the Bombyx mori pheromone-binding protein and its ligand, bombykol. The protein–ligand interaction of this molecular complex was minutely analyzed by the FMO method, and the analysis revealed several important interactions between the ligand and amino acid residues. [Copyright &y& Elsevier]

A quantum molecular simulation method applicable to biological molecules is proposed. Ab initio fragment molecular orbital method-based molecular dynamics (FMO-MD) combines molecular dynamics simulation with the ab initio fragment molecular orbital method. Here, FMO computes the force acting on each atom’s nucleus while MD computes the nuclei’s time-dependent evolutions. FMO-MD successfully simulated a small polypeptide, demonstrating the method’s applicability to biological molecules. [Copyright &y& Elsevier]

Recently, we have proposed the fragment molecular orbital (FMO) method; an approximate MO method for calculating large molecules such as proteins. The method has been shown to reproduce ab initio total energies and geometries of molecules in good accuracy. The most time consuming part in the method, the calculations of environmental electrostatic potentials, were speeded up by employing the Mulliken approximation for two-electron integrals and a fractional point charge approximation. Numerical calculations on several polypeptides revealed that the approximations brought no significant loss of accuracy in the total energy of molecules and were of practical use. [Copyright &y& Elsevier]